Supplementary Notebook S1B


STREAM SCoPE2 analysis performed on a monoctye differentiation dataset (Specht et al., 2020)

The processed result of this datasest is shown in Supplementary Figure 1B of the manuscript.

Preprint: Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity

Raw Data: link

Read in data

Preprocess

It is preprocessed data and there is no need to do filter and normalization again.

Feature selection

Dimension Reduction

Trajectory Inference

Trajectory Visulization

flat tree
Stream plot at single cell
stream plot

Marker genes detection

1) detect marker genes for each leaf branch
2) detect transition genes for each branch
3) detect marker genes that are differentially expressed between pairs of branches
4) detect cell population-specific markers

save results

Depending on the desired annotations and genes to be visualized by the user, the following command can be executed to create singlecellVR-compatible .JSON object.

scvr -f ./stream_result_var.pkl -t STREAM -a ANNOTATIONS [-g GENES] [-o OUTPUT]